High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic (Q28279911)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23180419%20AND%20SRC:MED&resulttype=core&format=json

18 February 2020

title

High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23180419%20AND%20SRC:MED&resulttype=core&format=json

18 February 2020

main subject

pandemic

0 references

1918-1920 flu pandemic

1 reference

1 reference

1 reference

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23180419%20AND%20SRC:MED&resulttype=core&format=json

18 February 2020

5

James M Musser

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23180419%20AND%20SRC:MED&resulttype=core&format=json

18 February 2020

6

Jeffery K Taubenberger

1 reference

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18 February 2020

4

Zong-Mei Sheng

1 reference

18 February 2020

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23180419%20AND%20SRC:MED&resulttype=core&format=json

Yong-Li Xiao

1

1 reference

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18 February 2020

John C Kash

series ordinal

2

1 reference

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18 February 2020

language of work or name

English

0 references

publication date

1 March 2013

1 reference

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18 February 2020

1 reference

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18 February 2020

volume

229

1 reference

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18 February 2020

issue

4

1 reference

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18 February 2020

page(s)

535-545

1 reference

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Integrative analysis of environmental sequences using MEGAN4

18 February 2020

cites work

1 reference

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Construction of normalized RNA-seq libraries for next-generation sequencing using the crab duplex-specific nuclease

20 March 2017

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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

20 March 2017

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Profiling critical cancer gene mutations in clinical tumor samples

20 March 2017

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The Sequence Alignment/Map format and SAMtools

20 March 2017

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Pandemic potential of a strain of influenza A (H1N1): early findings

20 March 2017

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TopHat: discovering splice junctions with RNA-Seq

20 March 2017

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Predominant role of bacterial pneumonia as a cause of death in pandemic influenza: implications for pandemic influenza preparedness

20 March 2017

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20 March 2017

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The pathology of influenza virus infections

20 March 2017

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MEGAN analysis of metagenomic data

20 March 2017

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Aberrant innate immune response in lethal infection of macaques with the 1918 influenza virus

20 March 2017

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Genomic analysis of increased host immune and cell death responses induced by 1918 influenza virus

20 March 2017

1 reference

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GENE SEQUENCING: The Race for the $1000 Genome

20 March 2017

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Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution

20 March 2017

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Orthomyxovirus replication, transcription, and polyadenylation.

20 March 2017

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Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis

20 March 2017

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Origin and evolution of the 1918 "Spanish" influenza virus hemagglutinin gene

20 March 2017

1 reference

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

20 March 2017

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Initial genetic characterization of the 1918 "Spanish" influenza virus

20 March 2017

1 reference

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Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic

20 March 2017

1 reference

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Gene expression profiles from formalin fixed paraffin embedded breast cancer tissue are largely comparable to fresh frozen matched tissue

20 March 2017

1 reference

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A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America

20 March 2017

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ABySS: a parallel assembler for short read sequence data

20 March 2017

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Emergence of a novel swine-origin influenza A (H1N1) virus in humans

7 April 2017

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Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans

7 April 2017

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In vivo evaluation of pathogenicity and transmissibility of influenza A(H1N1)pdm09 hemagglutinin receptor binding domain 222 intrahost variants isolated from a single immunocompromised patient

7 April 2017

1 reference

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Distinguishing characteristics between pandemic 2009-2010 influenza A (H1N1) and other viruses in patients hospitalized with respiratory illness

29 September 2017

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Autopsy series of 68 cases dying before and during the 1918 influenza pandemic peak

29 September 2017

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Insights on influenza pathogenesis from the grave

29 September 2017

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Paraffin embedding contributes to RNA aggregation, reduced RNA yield, and low RNA quality

29 September 2017

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Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq

29 September 2017

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Whole-transcriptome RNAseq analysis from minute amount of total RNA.

29 September 2017

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Pandemic influenza: certain uncertainties

29 September 2017

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Sequence-specific error profile of Illumina sequencers

29 September 2017

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The effect of formaldehyde fixation on RNA: optimization of formaldehyde adduct removal.

29 September 2017

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ECHO: a reference-free short-read error correction algorithm

29 September 2017

1 reference

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Excavation of a buried treasure--DNA, mRNA, miRNA and protein analysis in formalin fixed, paraffin embedded tissues

29 September 2017

1 reference

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Diagnosis of influenza from respiratory autopsy tissues: detection of virus by real-time reverse transcription-PCR in 222 cases

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731037

Hospitalized patients with 2009 pandemic influenza A (H1N1) virus infection in the United States--September-October 2009.

29 September 2017

1 reference

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Clinical and virological course of infection with haemagglutinin D222G mutant strain of 2009 pandemic influenza A (H1N1) virus

29 September 2017

1 reference

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Deep sequencing reveals mixed infection with 2009 pandemic influenza A (H1N1) virus strains and the emergence of oseltamivir resistance

29 September 2017

1 reference

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Pandemic swine-origin H1N1 influenza A virus isolates show heterogeneous virulence in macaques

29 September 2017

1 reference

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Influenza virus evolution, host adaptation, and pandemic formation

29 September 2017

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Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens

29 September 2017

1 reference

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Next generation sequencing in functional genomics

29 September 2017

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Prior infection with classical swine H1N1 influenza viruses is associated with protective immunity to the 2009 pandemic H1N1 virus

29 September 2017

1 reference

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Genomic signature and mutation trend analysis of pandemic (H1N1) 2009 influenza A virus

29 September 2017

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Complete-proteome mapping of human influenza A adaptive mutations: implications for human transmissibility of zoonotic strains.

29 September 2017

1 reference

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Pulmonary pathologic findings of fatal 2009 pandemic influenza A/H1N1 viral infections

29 September 2017

1 reference

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3'-end sequencing for expression quantification (3SEQ) from archival tumor samples

29 September 2017

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Lung abscess and pleuritis caused by Lactobacillus rhamnosus in an immunocompetent patient

29 September 2017

1 reference

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Streptococcus pneumoniae coinfection is correlated with the severity of H1N1 pandemic influenza.

29 September 2017

1 reference

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Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples

29 September 2017

1 reference

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The feasibility of using high resolution genome sequencing of influenza A viruses to detect mixed infections and quasispecies

29 September 2017

1 reference

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Pandemic influenza--including a risk assessment of H5N1

29 September 2017

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29 September 2017

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Pathology of human influenza revisited.

21 January 2018

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Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach

29 September 2017

1 reference

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Tissue handling and specimen preparation in surgical pathology: issues concerning the recovery of nucleic acids from formalin-fixed, paraffin-embedded tissue

29 September 2017

1 reference

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Detection of viral RNA from paraffin-embedded tissues after prolonged formalin fixation.

29 September 2017

1 reference

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RNA expression analysis from formalin fixed paraffin embedded tissues

29 September 2017

1 reference

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Mutational analyses of packaging signals in influenza virus PA, PB1, and PB2 genomic RNA segments

29 September 2017

1 reference

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Discovery and characterization of the 1918 pandemic influenza virus in historical context.

29 September 2017

1 reference

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The influenza virus resource at the National Center for Biotechnology Information

29 September 2017

1 reference

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Using RRT-PCR analysis and virus isolation to determine the prevalence of avian influenza virus infections in ducks at Minto Flats State Game Refuge, Alaska, during August 2005.

29 September 2017

1 reference

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Avian influenza virus exhibits rapid evolutionary dynamics

29 September 2017

1 reference

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Novel origin of the 1918 pandemic influenza virus nucleoprotein gene.

29 September 2017

1 reference

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Simple cDNA normalization using kamchatka crab duplex-specific nuclease

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731037

1918 influenza pandemic caused by highly conserved viruses with two receptor-binding variants.

29 September 2017

1 reference

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Updating the Accounts: Global Mortality of the 1918-1920 "Spanish" Influenza Pandemic

29 September 2017

1 reference

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Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731037

Optimization of the Isolation and Amplification of RNA From Formalin-fixed, Paraffin-embedded Tissue: The Armed Forces Institute of Pathology Experience and Literature Review

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731037

The position 4 nucleotide at the 3' end of the influenza virus neuraminidase vRNA is involved in temporal regulation of transcription and replication of neuraminidase RNAs and affects the repertoire of influenza virus surface antigens

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731037

Effects of fixative and fixation time on the extraction and polymerase chain reaction amplification of RNA from paraffin-embedded tissue. Comparison of two housekeeping gene mRNA controls

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731037

Characterization of the RNA-fork model of virion RNA in the initiation of transcription in influenza A virus

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731037

Adherence of Pseudomonas aeruginosa to tracheal cells injured by influenza infection or by endotracheal intubation.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731037

Human Fecal Flora: The Normal Flora of 20 Japanese-Hawaiians

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731037

29 September 2017

Formaldehyde fixation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731037

Improved base calling for the Illumina Genome Analyzer using machine learning strategies

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731037

Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731037

Universal primer set for the full-length amplification of all influenza A viruses

2 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPATH.4145

Global gene expression profiling of formalin-fixed paraffin-embedded tumor samples: a comparison to snap-frozen material using oligonucleotide microarrays

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23180419

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

DNA extraction from formalin-fixed, paraffin-embedded tissue

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23180419

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PATH.4145

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23180419%20AND%20SRC:MED&resulttype=core&format=json

18 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23180419%20AND%20SRC:MED&resulttype=core&format=json

18 February 2020

PubMed publication ID

23180419

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23180419%20AND%20SRC:MED&resulttype=core&format=json